Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

feat: json and tsv format support #26

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Conversation

almutlue
Copy link
Contributor

@almutlue almutlue commented Mar 25, 2025

Changes

Add support for json and tsv data formats.

  • gives the requested flexibility to add processed massspec data without relying on mzTab.
  • allows adding "support files" e.g., to store metadata for EGA submission

Limitations

  • this changes the scope of the DataFormat enumeration from omics-specific formats to general data formats.
  • does not include yaml and csv, because I don't want to add more formats than really necessary. Still csv might be a user request for EGA metadata submission?

Copy link

PR Preview Action v1.6.0

🚀 View preview at
https://sdsc-ordes.github.io/modos-schema/pr-preview/pr-26/

Built to branch gh-pages at 2025-03-25 08:03 UTC.
Preview will be ready when the GitHub Pages deployment is complete.

@almutlue almutlue requested a review from cmdoret March 25, 2025 08:30
@almutlue almutlue self-assigned this Mar 25, 2025
@almutlue almutlue added the enhancement New feature or request label Mar 25, 2025
@almutlue almutlue linked an issue Mar 25, 2025 that may be closed by this pull request
Copy link
Member

@cmdoret cmdoret left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Just one tiny issue with the format label (which requires regenerating the serializations).

But except for that, all good. Once fixed this can be merged 👍

@@ -312,3 +312,9 @@ enums:
mzTab:
description: tab-delimited format for mass spectrometry-based proteomics and metabolomics results.
meaning: EDAM:format_3681
TSV:
description: Comma-separated values format.
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
description: Comma-separated values format.
description: Tab-separated values format.

fix: format name (csv vs tsv)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Feature request: add support for json csv file format in DataEntity
2 participants